Invalid MEMLIMIT unit value with LSF jobs on Linux

[skoplev]

Invalid MEMLIMIT value with LSF on Linux

When running the tutorial example for HPC with LSF, caper submits invalid memory unit format. Is lower case 'g' but should be 'G', resulting in the following LSF error on Ubuntu:

caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name atac_seq_pipeline
2023-08-22 15:18:59,196|caper.hpc|INFO| Running shell command: bsub -W 2880 -M 4g -env all -J CAPER_atac_seq_pipeline /nfs/users/nfs_s/<userID>/lniu4in7.sh
MEMLIMIT value <4g> is not valid. Limit must be a positive integer. You can use the following units for the limit: KB (or K), MB (or M), GB (or G), TB (or T), PB (or P), EB (or E), ZB (or Z). Job not submitted.

OS/Platform

• OS/Platform: Ubuntu 18.04.6 LTS
• Conda version: conda 23.3.1
• Pipeline version: newest pulled from github
• Caper version: caper 2.3.2

Caper configuration file

Paste contents of ~/.caper/default.conf.

backend=lsf

# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=

cromwell=/nfs/users/nfs_s/<userID>/.caper/cromwell_jar/cromwell-82.jar
womtool=/nfs/users/nfs_s/<userID>/.caper/womtool_jar/womtool-82.jar

Input JSON file

Paste contents of your input JSON file.

https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json

[sbresnahan]

Bump

[hitz]

@akundaje any thoughts?

[akundaje]

Not sure. Seems like a Caper issue. Not familiar with its internals.